%A Seul-Ki Jeong
%A Min-Seok Kwon
%A Eun-Young Lee
%A Hyoung-Joo Lee
%A Sang Yun Cho
%A Hoguen Kim
%A Jong Shin Yoo
%A Gilbert S. Omenn
%A Ruedi Aebersold
%A Sam Hanash
%A Young-Ki Paik
%T BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 3729-3740
%V 9
%N 14
%U http://dx.doi.org/10.1002/pmic.200800593

%A Khan Z
%A Bloom JS
%A Garcia BA
%A Singh M
%A Kruglyak L
%T Protein quantification across hundreds of experimental conditions
%0 Journal Article
%D 2009
%J Proc Natl Acad Sci U S A
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19717460&dopt=Abstract
%8 Aug 26, 2009

%A Michel Schneider
%A Lydie Lane
%A Emmanuel Boutet
%A Damien Lieberherr
%A Michael Tognolli
%A Lydie Bougueleret
%A Amos Bairoch
%T The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
%0 Journal Article
%D 2009
%J Journal of Proteomics
%P 567-573
%V 72
%N 3
%U http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&_urlVersion=4&_origin=SDVIALERTASCII&_version=1&_uoikey=B8JDC-4V0MV8N-1&md5=7d50d597914e09d63062314b0e70c6cf

%A Shan He
%A Xiaoli Li
%A Mark R. Viant
%A Xin Yao
%T Profiling MS proteomics data using smoothed non-linear energy operator and Bayesian additive regression trees
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 4176-4191
%V 9
%N 17
%U http://dx.doi.org/10.1002/pmic.200800502

%A Networks Based on Interacting Domains
%T Proteome-wide Prediction of Signal Flow Direction in Protein Interaction
%0 Journal Article
%D 2009
%J Mol Cell Proteomics
%P 2063-2070
%V 8
%N 9
%U http://www.mcponline.org/cgi/content/abstract/8/9/2063?etoc

%A Meinicke P
%T UFO: a web server for ultra-fast functional profiling of whole genome protein sequences
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19725959&dopt=Abstract

%A Florian Reisinger
%A Lennart Martens
%T Database on Demand - An online tool for the custom generation of FASTA-formatted sequence databases
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 4421-4424
%V 9
%N 18
%U http://dx.doi.org/10.1002/pmic.200900254

%A Kevin Bleakley and Yoshihiro Yamanishi
%T Supervised prediction of drug-target interactions using bipartite local models
%0 Journal Article
%D 2009
%J Bioinformatics
%P 2397-2403
%V 25
%N 18
%U http://dx.doi.org/10.1093/bioinformatics/btp433

%A Liu Y
%T Feature extraction and dimensionality reduction for mass spectrometry data
%0 Journal Article
%D 2009
%J Comput Biol Med
%P 818-23
%V 39
%N 9
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19646687&dopt=Abstract

%A David Ovelleiro
%A Montserrat Carrascal
%A Vanessa Casas
%A Joaquin Abian
%T LymPHOS: Design of a phosphosite database of primary human T cells
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 3741-3751
%V 9
%N 14
%U http://dx.doi.org/10.1002/pmic.200800701

%A Hua-Mei Xin
%A Yuemin Zhu
%T Multiple information-based spot matching method for 2-DE images
%0 Journal Article
%D 2009
%J ELECTROPHORESIS
%P 2477-2480
%V 30
%N 14
%U http://dx.doi.org/10.1002/elps.200800453

%A Martin Eisenacher
%A Lennart Martens
%A Tanja Hardt
%A Michael Kohl
%A Harald Barsnes
%A Kenny Helsens
%A Jari Häkkinen
%A Fredrik Levander
%A Ruedi Aebersold
%A Joël Vandekerckhove
%A Michael J. Dunn
%A Frederique Lisacek
%A Jennifer A. Siepen
%A Simon J. Hubbard
%A Pierre-Alain Bi
%T Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 3928-3933
%V 9
%N 15
%U http://dx.doi.org/10.1002/pmic.200900247

%A Juan Antonio Vizcaíno
%A Richard Côté
%A Florian Reisinger
%A Joseph M. Foster
%A Michael Mueller
%A Jonathan Rameseder
%A Henning Hermjakob
%A Lennart Martens
%T A guide to the Proteomics Identifications Database proteomics data repository
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 4276-4283
%V 9
%N 18
%U http://dx.doi.org/10.1002/pmic.200900402

%A Aleksandar Stojmirovic and Yi-Kuo Yu
%T ITM Probe: analyzing information flow in protein networks
%0 Journal Article
%D 2009
%J Bioinformatics
%P 2447-2449
%V 25
%N 18
%U http://dx.doi.org/10.1093/bioinformatics/btp398

%A Xiaowen Liu
%A Yonghua Han
%A Denis Yuen
%A Bin Ma
%T Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
%0 Journal Article
%D 2009
%J Bioinformatics
%P 2174-2180
%V 25
%N 17
%U http://dx.doi.org/10.1093/bioinformatics/btp366

%A Li YF
%A Arnold RJ
%A Li Y
%A Radivojac P
%A Sheng Q
%A Tang H
%T A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics
%0 Journal Article
%D 2009
%J J Comput Biol
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19645593&dopt=Abstract
%8 Aug 1, 2009

%A Brylinski M
%A Skolnick J
%T Comparison of structure-based and threading-based approaches to protein functional annotation
%0 Journal Article
%D 2009
%J Proteins
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19731377&dopt=Abstract
%8 Aug 5, 2009

%A Harald Barsnes
%A Steffen Huber
%A Albert Sickmann
%A Ingvar Eidhammer
%A Lennart Martens
%T OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 3772-3774
%V 9
%N 14
%U http://dx.doi.org/10.1002/pmic.200900037

%A Martijn Dijkstra
%A Ritsert C. Jansen
%T Optimal analysis of complex protein mass spectra
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 3869-3876
%V 9
%N 15
%U http://dx.doi.org/10.1002/pmic.200701064

%A Hendrickson EL
%A Xia Q
%A Wang T
%A Lamont RJ
%A Hackett M
%T Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
%0 Journal Article
%D 
%J 
%P -
%V 
%N 
%U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=19723305&dopt=Abstract

%A Panagiotis Tsakanikas
%A Elias S. Manolakos
%T Improving 2-DE gel image denoising using contourlets
%0 Journal Article
%D 2009
%J PROTEOMICS
%P 3877-3888
%V 9
%N 15
%U http://dx.doi.org/10.1002/pmic.200701027

%A David S. DeLuca
%A Britta Eiz-Vesper
%A Nektarios Ladas
%A Barbara Anna-Maria Khattab
%A Rainer Blasczyk
%T High-throughput minor histocompatibility antigen prediction
%0 Journal Article
%D 2009
%J Bioinformatics
%P 2411-2417
%V 25
%N 18
%U http://dx.doi.org/10.1093/bioinformatics/btp404

%A Peptide Identity
%T Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign
%0 Journal Article
%D 2009
%J Mol Cell Proteomics
%P 2051-2062
%V 8
%N 9
%U http://www.mcponline.org/cgi/content/abstract/8/9/2051?etoc